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Many emerging embedded systems consist of multiple embedded nodes, which are connected through an internal small area network. In such systems, the synchronization between the embedded nodes is essential to provide real-time cooperation environment. On small area networks, the severe obstacle for achieving real-time synchronization is the unpredictable overhead of the system software running on the embedded nodes. This is true especially if a traditional operating system has been installed. Despite of these drawbacks, it is quite common to run traditional operating systems on some of the embedded nodes to utilize various existing applications. In this paper, we propose a novel design of communication primitives called RTDiP-Sync for real-time distributed synchronization over small area networks. Experiment results show that the suggested design can minimize the communication overhead and provide better overhead prediction.